I want to use 2-column page template on shopby and brand pages

To show the products in 2 columns please do the following:

1) open file app/design/frontend/YOUR-PACKAGE/YOUR-THEME/layout/amasty/amshopby.xml

2) add lines
<reference name="root">
<action method="setTemplate"><template>page/2columns-left.phtml</template>

right after the line <amshopby_index_index>

3) Clear the cache.

See more details on Improved Layered Navigation page
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